Let me just make sure I understand what you're saying, because I am pretty sure it matches what I thought was happening in here.
In the state of New York, when a business forms as a Domestic Not-For-Profit Corporation, that is a type of C corporation. It states it very clearly on the incorporation documents. My assumption, and I believe yours, is that because the entity does not yet have a federal 501c3 designation, despite being a type of not-for-profit in NY state, it is federally treated as a C corporation and would fill out a normal 1120.
My additional question that the NYS (and NYC) tax department cannot seem to answer is, are there different tax forms required for a not-for-profit corporation than for a for-profit corporation? It would be easy to just do the CTs, since they line up very well with the federal forms we'll be filing, but clearly the state has a unique designation for this type of business, so it's strange that there isn't more guidance from the state tax department.
